[gmx-users] Different Results with Different Platforms

[jkrieger at mrc-lmb.cam.ac.uk]

That is not a bug. The idea of NVT is it keeps your volume constant not
your pressure. In theory the pressure should stay fairly constant for a
given temperature as the solvent pushes against the boundaries or itself
to a fairly constant extent that depends on its velocities. I have not
however heard of anyone usually pressure coupling (NPT) for equilibration
only but I imagine it should work. You'd probably be best to keep the
velocities to be sure rather than generating them again. Did you not use
the same mdp files in the same order on all machines?

Best wishes
James

> As advised, I compared the systems between the different platforms and
> found the bug.
> I had initially equilibrated the pressure of my system in an NPT run
> before
> doing an NVT run on my desktop.
> Unbeknownst to me,  editconf had adjusted the coordinates of my molecules
> such that the pressure during the NVT run was almost 3 orders of magnitude
> higher than the initially equilibrated pressure, hence the unusual
> behaviour.
> I just did an NPT run on my desktop and it is loooking good.
> This bug cost me some frustrating weeks of my life but on the bright side,
> I may just get a publication from studying  it. :D
>
> Thank you so, so much Mark, Justin and Szilárd.
> I really appreciate your assistance!
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